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0
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1 /*
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2 * Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University
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3 * All rights reserved.
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4 *
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5 * Redistribution and use in source and binary forms, with or without modification,
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6 * are permitted provided that the following conditions are met:
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7 *
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8 * Redistributions of source code must retain the above copyright notice, this list
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9 * of conditions and the following disclaimer.
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10 * - Redistributions in binary form must reproduce the above copyright notice, this
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11 * list of conditions and the following disclaimer in the documentation and/or other
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12 * materials provided with the distribution.
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13 * - Neither the name of the <ORGANIZATION> nor the names of its contributors may be
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14 * used to endorse or promote products derived from this software without specific
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15 * prior written permission.
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16 *
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17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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28 */
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29
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30 /*
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31 * Author : Faraz Hach
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32 * Email : fhach AT cs DOT sfu
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33 * Last Update : 2009-12-08
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34 */
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35
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36
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37 #include <stdio.h>
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38 #include <stdlib.h>
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39 #include <string.h>
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40 #include <math.h>
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41 #include "Common.h"
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42 #include "RefGenome.h"
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43 #include "HashTable.h"
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44 /**********************************************/
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45 FILE *_ih_fp = NULL;
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46 IHashTable *_ih_hashTable = NULL;
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47 int _ih_maxHashTableSize = 0;
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48 char *_ih_refGen = NULL;
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49 char *_ih_refGenName = NULL;
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50 long long _ih_memUsage = 0;
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51 int _ih_refGenOff = 0;
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52 /**********************************************/
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53
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54 int hashVal(char *seq)
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55 {
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56 int i=0;
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57 int val=0, numericVal=0;
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58
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59 while(i<WINDOW_SIZE)
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60 {
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61 switch (seq[i])
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62 {
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63 case 'A':
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64 numericVal = 0;
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65 break;
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66 case 'C':
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67 numericVal = 1;
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68 break;
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69 case 'G' :
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70 numericVal = 2;
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71 break;
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72 case 'T':
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73 numericVal = 3;
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74 break;
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75 default:
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76 return -1;
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77 break;
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78 }
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79 val = (val << 2)|numericVal;
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80 i++;
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81 }
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82 return val;
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83 }
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84 /**********************************************/
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85 void freeIHashTableContent(IHashTable *hashTable, unsigned int maxSize)
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86 {
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87 int i=0;
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88 for (i=0; i<maxSize; i++)
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89 {
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90 if (hashTable[i].locs != NULL)
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91 {
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92 freeMem(hashTable[i].locs, (hashTable[i].locs[0]+1)*(sizeof(unsigned int)));
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93 hashTable[i].locs = NULL;
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94 }
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95 }
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96 }
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97 /**********************************************/
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98 void initSavingIHashTable(char *fileName)
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99 {
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100 int tmp;
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101 _ih_fp = fileOpen(fileName, "w");
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102 unsigned char bIndex = 0; // Bisulfite Index
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103
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104 // First Two bytes are indicating the type of the index & window size
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105 tmp = fwrite(&bIndex, sizeof(bIndex), 1, _ih_fp);
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106 tmp = fwrite(&WINDOW_SIZE, sizeof(WINDOW_SIZE), 1, _ih_fp);
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107
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108 }
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109 /**********************************************/
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110 void finalizeSavingIHashTable()
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111 {
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112 fclose(_ih_fp);
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113 }
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114 /**********************************************/
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115 void saveIHashTable(IHashTable *hashTable, unsigned int size, unsigned int maxSize, char *refGen, char *refGenName, int refGenOffset)
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116 {
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117 int tmp;
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118
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119 // Every Chunk starts with a byte indicating whether it has extra info;
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120 unsigned char extraInfo = 0;
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121 tmp = fwrite (&extraInfo, sizeof(extraInfo), 1, _ih_fp);
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122
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123 short len = strlen(refGenName);
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124 tmp = fwrite(&len, sizeof(len), 1, _ih_fp);
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125 tmp = fwrite(refGenName, sizeof(char), len, _ih_fp);
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126
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127 tmp = fwrite(&refGenOffset, sizeof(refGenOffset), 1, _ih_fp);
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128
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129 unsigned int refGenLength = strlen(refGen);
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130 tmp = fwrite(&refGenLength, sizeof(refGenLength), 1, _ih_fp);
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131 tmp = fwrite(refGen, sizeof(char), refGenLength, _ih_fp);
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132
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133 tmp = fwrite(&size, sizeof(size), 1, _ih_fp);
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134
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135 int i=0,j=0;
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136 unsigned char cnt=0;
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137 for (i=0; i<maxSize; i++)
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138 {
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139 if (hashTable[i].locs != NULL)
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140 {
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141 tmp = fwrite(&i, sizeof(i), 1, _ih_fp);
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142
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143 if (hashTable[i].locs[0] < 250)
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144 {
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145 cnt = hashTable[i].locs[0];
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146 tmp = fwrite(&cnt, sizeof(cnt), 1, _ih_fp);
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147 }
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148 else
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149 {
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150 cnt =0;
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151 tmp = fwrite (&cnt, sizeof(cnt), 1, _ih_fp);
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152 tmp = fwrite (&(hashTable[i].locs[0]), sizeof(hashTable[i].locs[0]), 1, _ih_fp);
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153 }
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154
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155 for (j=1; j<=hashTable[i].locs[0]; j++)
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156 tmp = fwrite(&(hashTable[i].locs[j]), sizeof(hashTable[i].locs[j]), 1, _ih_fp);
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157 }
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158 }
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159 }
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160 /**********************************************/
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161 unsigned int addIHashTableLocation(IHashTable *hashTable, int hv, int location)
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162 {
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163 unsigned int sizeInc = 0;
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164
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165 if (hashTable[hv].locs == NULL)
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166 {
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167 sizeInc = 1;
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168 hashTable[hv].locs = getMem (sizeof(unsigned int)*2);
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169 hashTable[hv].locs[0]=1;
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170 hashTable[hv].locs[1]=location;
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171 }
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172 else
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173 {
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174 int size = hashTable[hv].locs[0];
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175 int i;
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176 unsigned int *tmp = getMem( (size + 2) * sizeof(unsigned int) );
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177
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178 for (i = 0; i <= size; i++)
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179 {
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180 tmp[i] = hashTable[hv].locs[i];
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181 }
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182 size++;
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183 tmp[0] = size;
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184 tmp[size] = location;
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185
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186 freeMem(hashTable[hv].locs, (hashTable[hv].locs[0]*(sizeof(unsigned int))));
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187 hashTable[hv].locs = tmp;
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188 }
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189 return sizeInc;
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190 }
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191 /**********************************************/
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192 void generateIHashTable(char *fileName, char *indexName)
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193 {
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194 double startTime = getTime();
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195 unsigned int hashTableSize = 0;
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196 unsigned int hashTableMaxSize = pow(4, WINDOW_SIZE);
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197 IHashTable *hashTable = getMem(sizeof(IHashTable)*hashTableMaxSize);
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198 char *refGenName;
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199 char *refGen;
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200 int refGenOff = 0;
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201 int i, hv, l, flag;
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202
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203
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204 for ( i = 0; i < hashTableMaxSize; i++)
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205 {
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206 hashTable[i].locs = NULL;
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207 }
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208
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209 //Loading Fasta File
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210 if (!initLoadingRefGenome(fileName))
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211 return;
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212 initSavingIHashTable(indexName);
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213
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214 fprintf(stdout, "Generating Index from %s", fileName);
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215 fflush(stdout);
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216
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217 char *prev = getMem (CONTIG_NAME_SIZE);
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218 prev[0]='\0';
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219
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220 do
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221 {
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222 flag = loadRefGenome (&refGen, &refGenName, &refGenOff);
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223
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224 if ( strcmp(prev, refGenName) != 0)
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225 {
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226 fprintf(stdout, "\n - %s ", refGenName);
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227 fflush(stdout);
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228 sprintf(prev, "%s", refGenName);
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229 }
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230 else
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231 {
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232 fprintf(stdout, ".");
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233 fflush(stdout);
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234 }
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235
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236 l = strlen(refGen) - WINDOW_SIZE;
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237
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238 for (i=0; i < l; i++)
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239 {
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240 hv = hashVal(refGen + i);
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241 if (hv != -1)
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242 {
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243 hashTableSize += addIHashTableLocation (hashTable, hv, i+1);
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244 }
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245 }
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246
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247 saveIHashTable(hashTable, hashTableSize, hashTableMaxSize, refGen, refGenName, refGenOff);
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248 freeIHashTableContent(hashTable, hashTableMaxSize);
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249 hashTableSize = 0;
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250 } while (flag);
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251
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252 freeMem(prev, CONTIG_NAME_SIZE);
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253 freeMem(hashTable, sizeof(IHashTable)*hashTableMaxSize);
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254
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255 finalizeLoadingRefGenome();
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256 finalizeSavingIHashTable();
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257
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258 fprintf(stdout, "\nDONE in %0.2fs!\n", (getTime()-startTime));
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259 }
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260
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261 /**********************************************/
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262 void finalizeLoadingIHashTable()
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263 {
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264 freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
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265 freeMem(_ih_hashTable, sizeof(IHashTable)* _ih_maxHashTableSize);
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266 freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
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267 freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
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268 fclose(_ih_fp);
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269 }
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270
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271 /**********************************************/
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272 int loadIHashTable(double *loadTime)
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273 {
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274 double startTime = getTime();
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275 unsigned char extraInfo = 0;
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276 short len;
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277 unsigned int refGenLength;
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278 unsigned int hashTableSize;
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279 unsigned int tmpSize;
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280 int tmp;
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281 int i=0,j=0;
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282
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283 if ( fread(&extraInfo, sizeof(extraInfo), 1, _ih_fp) != sizeof(extraInfo) )
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284 return 0;
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285
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286 freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
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287 freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
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288 freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
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289
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290 // Reading Chr Name
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291 tmp = fread(&len, sizeof(len), 1, _ih_fp);
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292 _ih_refGenName = getMem(sizeof(char)* (len+1));
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293 tmp = fread(_ih_refGenName, sizeof(char), len, _ih_fp);
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294 _ih_refGenName [len] ='\0';
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295
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296 tmp = fread(&_ih_refGenOff, sizeof (_ih_refGenOff), 1, _ih_fp);
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297
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298 // Reading Size and Content of Ref Genome
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299 tmp = fread(&refGenLength, sizeof(refGenLength), 1, _ih_fp);
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300 _ih_refGen = getMem(sizeof(char)*(refGenLength+1));
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301 tmp = fread(_ih_refGen, sizeof(char), refGenLength, _ih_fp);
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302 _ih_refGen[refGenLength]='\0';
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303
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304 //Reading Hashtable Size and Content
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305 tmp = fread(&hashTableSize, sizeof(hashTableSize), 1, _ih_fp);
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306
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307 unsigned int hv;
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308 unsigned char cnt=0;
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309 for (i=0; i<hashTableSize; i++)
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310 {
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311 tmp = fread(&hv, sizeof(hv), 1, _ih_fp);
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312 tmp = fread(&cnt, sizeof(cnt), 1, _ih_fp);
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313
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314 if (cnt>0)
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315 {
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316 tmpSize = cnt;
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317 }
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318 else
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319 {
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320 tmp = fread(&tmpSize, sizeof(tmpSize), 1, _ih_fp);
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321 }
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322
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323 _ih_hashTable[hv].locs = getMem( sizeof(unsigned int)* (tmpSize+1) );
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324 _ih_hashTable[hv].locs[0] = tmpSize;
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325
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326 for (j=1; j<=tmpSize; j++)
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327 tmp = fread(&(_ih_hashTable[hv].locs[j]), sizeof(_ih_hashTable[hv].locs[j]), 1, _ih_fp);
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328 }
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329 *loadTime = getTime()-startTime;
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330
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331 return 1;
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332 }
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333 /**********************************************/
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334 unsigned int *getIHashTableCandidates(int hv)
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335 {
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336 if ( hv != -1 )
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337 return _ih_hashTable[hv].locs;
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338 else
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339 return NULL;
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340 }
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341 /**********************************************/
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342 /**********************************************/
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343 /**********************************************/
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344 void configHashTable()
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345 {
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346 if (WINDOW_SIZE <= 14)
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347 {
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348 generateHashTable = &generateIHashTable;
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349 loadHashTable = &loadIHashTable;
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350 finalizeLoadingHashTable = &finalizeLoadingIHashTable;
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351 getCandidates = &getIHashTableCandidates;
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352 }
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353 else
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354 {
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355
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356
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357 }
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358 }
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359 /**********************************************/
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360 int initLoadingHashTable(char *fileName)
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361 {
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362 int i;
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363 unsigned char bsIndex;
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364 int tmp;
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365
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366 _ih_fp = fileOpen(fileName, "r");
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367
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368 if (_ih_fp == NULL)
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369 return 0;
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370
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371 tmp = fread(&bsIndex, sizeof(bsIndex), 1, _ih_fp);
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372 if (bsIndex)
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373 {
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374 fprintf(stdout, "Error: Wrong Type of Index indicated");
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375 return 0;
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376 }
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377
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378 tmp = fread(&WINDOW_SIZE, sizeof(WINDOW_SIZE), 1, _ih_fp);
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379
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380 configHashTable();
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381
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382 if (_ih_maxHashTableSize != pow(4, WINDOW_SIZE))
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383 {
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384
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385 if (_ih_hashTable != NULL)
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386 {
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387 freeIHashTableContent(_ih_hashTable, _ih_maxHashTableSize);
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388 freeMem(_ih_hashTable, sizeof(IHashTable)* _ih_maxHashTableSize);
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389 freeMem(_ih_refGen, strlen(_ih_refGen)+1) ;
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390 freeMem(_ih_refGenName, strlen(_ih_refGenName)+1);
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391 }
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392
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393 _ih_maxHashTableSize = pow(4, WINDOW_SIZE);
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394
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395 _ih_hashTable = getMem (sizeof(IHashTable) * _ih_maxHashTableSize);
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396 for (i=0; i<_ih_maxHashTableSize; i++)
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397 _ih_hashTable[i].locs = NULL;
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398 _ih_refGen = getMem(1);
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399 _ih_refGen[0]='\0';
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400 _ih_refGenName = getMem(1);
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401 _ih_refGenName[0] = '\0';
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402 }
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403
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404 return 1;
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405 }
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406 /**********************************************/
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407 char *getRefGenome()
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408 {
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409 return _ih_refGen;
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410
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411 }
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412 /**********************************************/
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413 char *getRefGenomeName()
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414 {
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415 return _ih_refGenName;
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416
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417 }
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418 /**********************************************/
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419 int getRefGenomeOffset()
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420 {
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421 return _ih_refGenOff;
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422
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423 }
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424 /**********************************************/
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425 HashTable *getHashTable()
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426 {
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427 return NULL;
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428 }
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